#include "mothur.h"
-#include "sparsematrix.hpp"
+#include "sequence.hpp"
-typedef list<PCell>::iterator MatData;
-typedef map<int, float> SeqMap; //maps sequence to all distance for that seqeunce
+/***********************************************************************/
+struct Preference {
+ string name;
+ vector<string> leftParent; //keep the name of closest left associated with the two scores
+ vector<string> rightParent; //keep the name of closest right associated with the two scores
+ vector<float> score; //so you can keep last score and calc this score and keep whichever is bigger.
+ vector<float> closestLeft; //keep the closest left associated with the two scores
+ vector<float> closestRight; //keep the closest right associated with the two scores
+ int midpoint;
+
+};
+/***********************************************************************/
+struct score_struct {
+ int prev;
+ int score;
+ int row;
+ int col;
+};
+/***********************************************************************/
+struct trace_struct {
+ int col;
+ int oldCol;
+ int row;
+};
+/***********************************************************************/
+struct results {
+ int regionStart;
+ int regionEnd;
+ int nastRegionStart;
+ int nastRegionEnd;
+ string parent;
+ float queryToParent;
+ float queryToParentLocal;
+ float divR;
+};
+/***********************************************************************/
+struct SeqDist {
+ Sequence* seq;
+ float dist;
+};
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareRegionStart(results left, results right){
+ return (left.nastRegionStart < right.nastRegionStart);
+}
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSeqDist(SeqDist left, SeqDist right){
+ return (left.dist < right.dist);
+}
+//********************************************************************************************************************
+struct sim {
+ string leftParent;
+ string rightParent;
+ float score;
+ int midpoint;
+};
+
+struct linePair {
+ int start;
+ int end;
+ linePair(int i, int j) : start(i), end(j) {}
+ linePair(){}
+};
/***********************************************************************/
Chimera(){};
Chimera(string);
+ Chimera(string, string);
virtual ~Chimera(){};
- virtual void setFilter(bool f) { filter = f; }
+ virtual void setFilter(bool f) { filter = f; }
virtual void setCorrection(bool c) { correction = c; }
virtual void setProcessors(int p) { processors = p; }
virtual void setWindow(int w) { window = w; }
virtual void setIncrement(int i) { increment = i; }
- virtual void setTemplate(string t) { templateFile = t; }
+ virtual void setNumWanted(int n) { numWanted = n; }
+ virtual void setKmerSize(int k) { kmerSize = k; }
+ virtual void setSVG(int s) { svg = s; }
+ virtual void setName(string n) { name = n; }
+ virtual void setMatch(int m) { match = m; }
+ virtual void setMisMatch(int m) { misMatch = m; }
+ virtual void setDivR(float d) { divR = d; }
+ virtual void setParents(int p) { parents = p; }
+ virtual void setMinSim(int s) { minSim = s; }
+ virtual void setMinCoverage(int c) { minCov = c; }
+ virtual void setMinBS(int b) { minBS = b; }
+ virtual void setMinSNP(int s) { minSNP = s; }
+ virtual void setIters(int i) { iters = i; }
+ virtual void setTemplateSeqs(vector<Sequence*> t) { templateSeqs = t; }
+ virtual bool getUnaligned() { return unaligned; }
+ virtual void setTemplateFile(string t) { templateFileName = t; }
+
+ virtual void setCons(string){};
+ virtual void setQuantiles(string){};
+ virtual void doPrep(){};
+ virtual vector<Sequence*> readSeqs(string);
+ virtual vector< vector<float> > readQuantiles();
+ virtual void setMask(string);
+ virtual void runFilter(Sequence*);
+ virtual void createFilter(vector<Sequence*>);
+
+ virtual void printHeader(ostream&){};
+ virtual int getChimeras(Sequence*){ return 0; }
+ virtual int getChimeras(){ return 0; }
+ virtual void print(ostream&){};
- //pure functions
- virtual void getChimeras() = 0;
- virtual void print(ostream&) = 0;
protected:
- bool filter, correction;
- int processors, window, increment;
- string templateFile;
-
-
+ vector<Sequence*> templateSeqs;
+ bool filter, correction, svg, unaligned;
+ int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters;
+ float divR;
+ string seqMask, quanfile, filterString, name, outputDir, templateFileName;
+ Sequence* getSequence(string); //find sequence from name
};
/***********************************************************************/